I have encountered a problem while working with Agilent 4x44k whole mouse genome v2 microarray chips.
A part of my experiment was performed 1.5 years ago (pilot study), and the second part - just now.
All the data obtained from the both parts of the experiment has been background-corrected and normalized with limma. I performed a backgroundCorrect(method="normexp") and than used normalizeBetweenArrays(method="quantile").
The data from different parts of the experiment forms two distinctive clusters ("new" and "old") in the Principle component analysis (PCA), even though the samples are supposed to be the same and come from the same origin.
Did i oversee some requirements? Are the normalization/background correction methods more suitable to this kind of problems? Thank you!